A “pin” is an input or output on the Smoothieboard.

In a lot of cases ( step/direction for external stepper motors, button inputs ), you can use any pin for any use.

If other cases, a given pin is tied to a given peripheral on the board.

See Pinout to learn about which pins are where.

You can have a pin's output inverted by adding a “!” after this pin's number in the config line, example : 

my_pin_name                      19!

There are other modifiers for pins :

All options

! Exclamation mark Invert pin
o Lowercase O letter Set pin to open drain
^ Caret, Shift+6 on QWERTY keyboards Set pin to pull up (Default on most pins)
v Lowercase v letter Set pin to pull down
- Minus sign To set no pullup
@ At / Arobase sign To set repeater mode
Nothing No modifier, if you do not set any option/modifier for your pin, it will be in pullup mode as if it had ^ specified

Hard-wired

Note some pins have hardware on the board itself, enforcing a given configuration.

The main example of this is the endstop inputs, which have on-board pull-up resistors, which means trying to deactivate pull-ups in configuration (- for them will not work

(configuration can not deactivate/remove physically present pull-up resistors, it can only act on pull-up pin-configuration peripherals “inside” the chip ).